Johannes Debler

BRAKER2 Guessing the location of $GENEMARK_PATH failed.

1

Hi, I am trying to run Braker2 2.1.6--hdfd78af_5 but am running into a problem with the genemark path. ```# Thu Oct 14 07:06:50 2021: Did not find environment variable $GENEMARK_PATH...

Problems downloading from gdrive and dropbox

1

I get errors importing from gdrive and Dropbox on version 10.9.993. Gdrive error message : 401. That’s an error. Error: invalid_client The OAuth client was invalid. Request Details client_id= response_type=code...

cannot index extracted contigs

2

Hi, I extracted individual contigs from a bam file using: `BamDeal_Linux modify bamSplit -r -i me14.sorted.again.bam` and `BamDeal_Linux modify bamSplit -i me14.sorted.again.bam` However, when I try to index the extracted...

Contact info not turned into links

3

Hi there, The github, twitter, linkedin and website lines in the 'Contact' section are only turned into functional links if you put the full URL in the google spreadsheet. That...

KeyError: 'antismash_generation'

2

**Are you using the latest release?** 1.8.15 via conda **What command did you issue?** funannotate remote -i funannotate_output -m antismash -e [email protected] **Logfiles** funannotate-remote.log ``` [05/04/23 00:18:33]: /home/ubuntu/mambaforge/envs/funannotate/bin/funannotate remote -i...

highlighting telomeres (adding custom symbols to chromosome ends)

3

Hi, I recently saw a graph in a paper that looked like a KaryploteR image where the authors added something to all the chromosome ends that had telomeres to show...

telomeres getting lost

6

**Describe the bug** I was running a comparison of current long read assemblers and realised that NextDenovo has one of the best contiguities, however, it seems to trim a lot...

Hi, I seem to be unable to `pb set-key` as I keep getting this error message: ``` johannes@cicer:~$ pb set-key Enter your security token from https://www.pushbullet.com/account: Traceback (most recent call...

Hi, I can't find the precompiled binaries as mentioned in the Readme and I'm having problems compiling it myself. The release page only contains the sourcecode. Cheers

2.9.3 docker crashes

2

Hi, I have tried running the latest flye as a docker image from quai.io (https://quay.io/repository/biocontainers/flye?tab=tags&tag=2.9.3--py310h2b6aa90_0). It keeps crashing with below error. I have retried the older version 2.9.2 from quai.io...